In pbs-assess/PACea: An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management

Summary

Commitments from package authors

We will:

• \tiny (try to) \normalsize not break the package, by working on branches on GitHub before merging.

• ensure any improvements are back compatible.

• update the NEWS as we add/update data and make improvements.

• ideally update the following r colorize("on the 20th of every month (or soon after)", "red") to get the latest raw data:

• climatic and oceanographic indices
• buoy sst
• OISST

Commitments from package authors

• update other data as appropriate:
• hake assessment output: February each year
• harbour seals: next time assessment is updated
• herring assessment output: when SAR published each year
• BCCM model output: the model may be run into 2020 (boundary conditions come from a global model currently only available to Jan 2021).
  • note that BCCM is a research model (not an operational model) so updates depend on projects and access to High Performance Computing.

Recommended guidelines for users

Please:

• read the README!!

• check the help files and vignettes

• check the NEWS (for updates to data, useful additions, new data, etc.)

• understand the limitations of the data

• cite pacea and the original sources for any data you use

```{asis, echo = more_details}

Recommended guidelines for users

To check when you last installed pacea

```r
pacea_installed()

You last locally installed pacea on 2023-11-01 which is 8 days ago.

Compare that with the updates in the NEWS file (and you can also check dates of the latest commits at
https://github.com/pbs-assess/pacea/commits/main)

knitr::include_graphics(paste0(here::here(),
                               "/talks/talks-manual-figures/github-commits.png"))

```{asis, echo = more_details}

Recommended guidelines for users

• any problems, make a minimum working example (usually makes you figure it out yourself)

• check the Issues on GitHub in case someone else has asked or we are already working on it

• simple quick question just ask us

• more detailed questions or bug reports post a new Issue (allows others to see, and maybe answer, your question)

<!-- see short version for maybe more -->
## Current uses of pacea (that we know about)

 - Spiny Dogfish: understanding declines over the past 20 years

 - shrimp: impact of including environmental variables on predicting distributions

 - humpback whales and porpoises: environmental covariates in species distribution models

 - Pacific Saury assessment: finding links between two basin-scale indices and process errors, directly supporting Canada's North Pacific Fisheries
   Commission commitments

## Lessons learned (applicable to other regions)

 - is possible to amaglamate different ecosystem information into one place

 - not an off-the-side-of-your-desk project

 - is being used by DFO scientists (and others)

 - infrastructure of the package could be utilised in other regions if
   interested
   - e.g. my monthly download of buoy data is for all Canadian waters,
   the data processing, storing, and plotting functions could be adopted
   - similarly for other types of data/information

## Summary

<!-- - let us know of any applications (so we understand the uptake and how much
   effort to devote to maintaining it)

   - you could be out on a survey and wondering how warm the water is
        compared to previous years

    - Chris Rooper: looking at Pacific Saury process errors from a stock assessment
 using the indices (PDO etc.). ``It made my life easier today."
-->
 - https://github.com/pbs-assess/pacea

 - installation:
   \textcolor{red}{\texttt{remotes::install\_github("pbs-assess/pacea")}}

\

\begin{center}
\includegraphics[width = 2cm]{"../man/figures/logo.png"}\\
\emph{We wrangle the data so you don't have to}
\end{center}

\

```r
citation("pacea")

Edwards AM, Tai TC, Watson J, Peña MA, Hilborn A, Hannah CG, Rooper CN
(2023). "pacea: An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management."
  https://github.com/pbs-assess/pacea.

pbs-assess/PACea documentation built on April 17, 2025, 11:36 p.m.